INFO 2025-06-26 20:08:20,999 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:08:20,999 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:08:20,999 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.297.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:08:20,999 process.py download_process():165 [1] Download and processing steps for 2013.297.02 INFO 2025-06-26 20:08:20,999 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013297/2013.297.02 INFO 2025-06-26 20:08:20,999 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013297/2013.297.02 to /data/auv_data/dorado/missionlogs/2013.297.02 INFO 2025-06-26 20:08:24,104 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.297.02 INFO 2025-06-26 20:08:24,104 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/ctdDriver.log (5231046 bytes) INFO 2025-06-26 20:08:24,471 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/ctdDriver2.log (5230943 bytes) INFO 2025-06-26 20:08:24,843 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/gps.log (50468 bytes) INFO 2025-06-26 20:08:24,856 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/hydroscatlog.log (4581550 bytes) INFO 2025-06-26 20:08:25,328 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/navigation.log (18517894 bytes) INFO 2025-06-26 20:08:26,618 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/parosci.log (6434534 bytes) INFO 2025-06-26 20:08:27,140 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.297.02/parosci.log: [15 16 23 25] INFO 2025-06-26 20:08:27,155 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/tailCone.log (3275803 bytes) INFO 2025-06-26 20:08:27,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/biolume.log (3814542 bytes) INFO 2025-06-26 20:08:27,936 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:08:28,127 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.02 seconds INFO 2025-06-26 20:08:28,128 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.297.02/lopc.bin (31348307 bytes) INFO 2025-06-26 20:08:28,128 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:08:28 2025 INFO 2025-06-26 20:08:28,128 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.297.02/parosci.nc INFO 2025-06-26 20:08:28,128 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:08:28,128 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.297.02/parosci.nc INFO 2025-06-26 20:08:28,131 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382638614.3, sensor_off_time = 1382652263.0 INFO 2025-06-26 20:08:28,131 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13648 seconds. Expecting to read 27296 L frames from the lopc.bin file. INFO 2025-06-26 20:08:28,131 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 27296 records from the lopc.bin file. INFO 2025-06-26 20:08:28,294 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-24 18:16:54 Z and endTime = 2013-10-24 22:04:23 Z with 27296 records expected to be read from lopc.bin INFO 2025-06-26 20:08:28,294 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.297.02/lopc.bin INFO 2025-06-26 20:08:28,294 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.297.02/lopc.nc INFO 2025-06-26 20:08:28,295 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.297.02/lopc.nc INFO 2025-06-26 20:08:28,295 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.297.02 INFO 2025-06-26 20:08:28,296 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:08:28,299 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:08:28,342 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:08:28,342 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:08:28,342 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:08:31,325 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:08:31,326 process.py calibrate():227 [1] Calibration steps for 2013.297.02 INFO 2025-06-26 20:08:31,471 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:08:31,473 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:08:32,012 calibrate.py _nudge_pos():1806 [1] 89: 0.170 -0.0003826 0.0017120 7040 23.46 -2.417 13.521 2013-10-24T18:41:46.514211072 INFO 2025-06-26 20:08:32,105 calibrate.py _nudge_pos():1806 [1] 99: 0.160 -0.0000010 -0.0000092 60 0.20 -0.726 -8.638 2013-10-24T18:42:07.522771968 INFO 2025-06-26 20:08:32,502 calibrate.py _nudge_pos():1806 [1] 142: 0.170 -0.0007419 0.0021366 8355 27.85 -3.949 14.218 2013-10-24T19:10:40.515424000 INFO 2025-06-26 20:08:32,863 calibrate.py _nudge_pos():1806 [1] 181: 0.180 -0.0007791 0.0022165 8595 28.65 -4.032 14.337 2013-10-24T19:39:58.514992896 INFO 2025-06-26 20:08:33,169 calibrate.py _nudge_pos():1806 [1] 214: 0.170 -0.0003734 0.0006005 2150 7.16 -7.728 15.534 2013-10-24T19:47:40.523343104 INFO 2025-06-26 20:08:33,650 calibrate.py _nudge_pos():1806 [1] 266: 0.170 0.0003459 0.0003519 4335 14.45 3.550 4.514 2013-10-24T20:02:58.520456192 INFO 2025-06-26 20:08:34,088 calibrate.py _nudge_pos():1806 [1] 313: 0.180 -0.0005741 -0.0000404 4240 14.13 -6.024 -0.530 2013-10-24T20:17:52.519213056 INFO 2025-06-26 20:08:34,416 calibrate.py _nudge_pos():1806 [1] 348: 0.190 -0.0010310 -0.0005337 6520 21.73 -7.033 -4.551 2013-10-24T20:40:10.517553920 INFO 2025-06-26 20:08:34,881 calibrate.py _nudge_pos():1806 [1] 398: 0.180 -0.0009598 -0.0006231 7015 23.38 -6.084 -4.938 2013-10-24T21:04:22.518084864 INFO 2025-06-26 20:08:35,276 calibrate.py _nudge_pos():1806 [1] 440: 0.190 -0.0011589 -0.0006477 7685 25.61 -6.704 -4.686 2013-10-24T21:30:40.519984128 INFO 2025-06-26 20:08:35,754 calibrate.py _nudge_pos():1806 [1] 491: 0.190 -0.0008804 -0.0004796 5390 17.96 -7.262 -4.947 2013-10-24T21:49:28.522710784 INFO 2025-06-26 20:08:36,083 calibrate.py _nudge_pos():1806 [1] 526: 0.190 -0.0003724 -0.0002394 3490 11.63 -4.745 -3.814 2013-10-24T22:01:40.522565376 INFO 2025-06-26 20:08:37,618 calibrate.py _nudge_pos():1862 [1] 651: - - - 1 0.00 - - INFO 2025-06-26 20:08:37,618 calibrate.py _nudge_pos():1868 [1] Points in final series = 67988 INFO 2025-06-26 20:08:40,228 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:08:40,739 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:08:41,155 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:08:41,156 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.297.02/ctd1.nc INFO 2025-06-26 20:08:41,158 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:08:41,158 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:08:41,158 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:08:41,716 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:08:42,120 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:08:42,122 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.297.02/ctd2.nc INFO 2025-06-26 20:08:42,124 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:08:42,124 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:08:42,124 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:08:42,124 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.297.02 INFO 2025-06-26 20:08:42,136 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:08:42,704 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 120 121 122 123 124 125] INFO 2025-06-26 20:08:42,824 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:08:55,108 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.297.02 ERROR 2025-06-26 20:08:55,108 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.297.02 INFO 2025-06-26 20:08:55,163 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_cal.nc INFO 2025-06-26 20:08:55,269 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:08:55,275 process.py align():251 [1] Alignment steps for 2013.297.02 INFO 2025-06-26 20:08:55,307 align.py process_cal():139 [1] Processing dorado_2013.297.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.297.02 INFO 2025-06-26 20:08:55,329 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:08:55,332 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:08:55,380 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:08:55,384 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:08:55,432 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:08:55,436 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:08:55,465 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:08:55,465 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:08:55,484 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:08:55,488 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:08:55,537 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,541 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,583 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,586 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,629 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,632 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,674 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,677 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,722 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,726 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,768 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,771 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,814 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,817 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,860 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,864 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,907 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,910 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,953 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:55,956 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:55,999 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,003 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,045 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,049 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,093 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,097 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,139 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,142 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,185 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,188 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,230 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,234 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,277 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,281 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,324 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,327 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,370 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,374 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,416 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,420 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,466 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,509 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.297.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:08:56,512 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:08:56,569 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:08:56,610 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:08:56,675 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:08:57,019 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:08:57,054 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_align.nc INFO 2025-06-26 20:08:57,161 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:08:57,163 process.py resample():273 [1] Resampling steps for 2013.297.02 INFO 2025-06-26 20:08:57,163 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:08:57,192 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_align.nc mission netCDF file INFO 2025-06-26 20:08:57,197 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_align.nc mission netCDF file INFO 2025-06-26 20:08:57,198 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-24T18:17:28.724076800 to 2013-10-24T22:04:22.921440256 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 20:08:57,200 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-24T18:17:03.835781888 to 2013-10-24T22:04:23.021433600 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:08:57,201 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-24T18:17:22.794482944 to 2013-10-24T22:04:23.021433600 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:08:57,203 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-24T18:17:22.954472192 to 2013-10-24T22:04:22.901441792 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:08:57,204 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-24T18:16:53.346466048 to 2013-10-24T22:04:21.781484032 (0 days 00:00:01.239949568 before mission_end) INFO 2025-06-26 20:08:57,205 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-24T18:16:55.016385792 to 2013-10-24T22:04:22.901441792 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:08:57,206 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_align.nc mission netCDF file INFO 2025-06-26 20:08:57,207 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,359 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,386 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,413 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,439 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,464 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,487 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,510 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,532 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,554 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,575 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,597 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,619 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,641 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,665 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,687 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,709 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,731 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,755 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,779 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,802 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,825 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,847 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,869 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,892 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,903 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,914 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:57,918 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:08:57,918 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:08:58,411 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:08:58,495 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:08:58,543 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:08:58,563 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:08:58,581 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:08:58,581 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:08:58,613 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:08:58,794 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_1S.nc INFO 2025-06-26 20:09:00,993 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:09:11,806 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.297.02/dorado_2013.297.02_1S_Gulper.txt INFO 2025-06-26 20:09:11,807 process.py archive():337 [1] Archiving steps for 2013.297.02 INFO 2025-06-26 20:09:11,807 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:09:11,808 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:09:11,809 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.297.02_1S.nc INFO 2025-06-26 20:09:11,825 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:09:11,826 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.297.02_cal.nc INFO 2025-06-26 20:09:11,920 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:09:11,921 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.297.02_align.nc INFO 2025-06-26 20:09:12,060 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:09:12,082 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,101 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,106 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,123 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,176 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,197 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,213 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,252 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,260 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013297/2013.297.02 done. INFO 2025-06-26 20:09:12,260 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:09:12,261 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.297.02_1S_Gulper.txt INFO 2025-06-26 20:09:12,267 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.297.02/dorado_2013.297.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:09:12,267 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.297.02/dorado_2013.297.02_processing.log /Volumes/AUVCTD/surveys/2013/netcdf